In a climate change scenario , relevant attention must be given to its impact on marine environments as well as transitional waters (e.g. coastal lagoons), with the aim of their conservation and sustainable use. The environmental changes are already undergoing and scientific knowledge is advancing about the factors affecting the structure and functioning of these ecosystems. The dataset is composed by in situ measurement by mean multiparametric probe CTD, manual sampling and lab analisys, in order  to investigate the impacts of climate change on water physico-chemical properties of  Lesina lagoon over a period of 14 years. Surface water temperature and salinity data were measured from 2010 to 2023 by a multiparametric probe (CTD) Hydrolab DS5. The measurements were carried out in a total of 38 sampling sites All the data collected were then processed according to the methodologies standardized by the probe manufacturer. The raw data were converted into engineering units based on precision and accuracy of the calibration process of the multiparametric probe, which takes place annually at the manufacturing company.